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Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
Alpha and beta diversity of an amplicon (16S/ITS) ASV/OTU community table - observed features, Shannon, Pielou evenness, Faith PD, Bray-Curtis, Jaccard, weighted/unweighted/generalized UniFrac, Aitchison/RPCA - via QIIME2 core-metrics-phylogenetic, phyloseq/vegan, and scikit-bio. Covers the three...
End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-...
End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/b...
Agent skill for Researcher, Data Scientist, published by GPTomics. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by FridrichMethod. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by FridrichMethod. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by FridrichMethod. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, published by FridrichMethod. Project details and file access are provided by the publisher.
Agent skill for Data Scientist, Researcher, published by FridrichMethod. Project details and file access are provided by the publisher.
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